Genetic diversity in - chilli (Capsicum annuum L.) based on microsatellite markers: An evaluation of Bangladeshi germplasm


  • Md. Rezwan MOLLA Bangladesh Agricultural Research Institute, Bangladesh
  • Iftekhar AHMED Bangladesh Agricultural Research Institute, Bangladesh
  • Md. Motiar ROHMAN Bangladesh Agricultural Research Institute, Bangladesh
  • Mohammad Amdadul HAQUE Bangladesh Agricultural Research Institute, Bangladesh
  • Shah Md. Monir HOSSAIN Bangladesh Agricultural Research Council, Bangladesh
  • Lutful HASSAN Bangladesh Agricultural University, Bangladesh



chilli, genetic diversity, microsatellite (SSR) markers, polymorphism information content


Genetic diversity analysis is a pre-requisite to develop improve variety of any crop. Hence, 39 SSR markers were used to analyze the genetic diversity of local chilli cultivars. PCR-amplified microsatellite loci were shown to be polymorphic in all investigated cultivars. The locus, CAMS-647 produced the highest number of alleles (8) ranging in size from 188 to 279 bp. PIC values for 39 primers ranged from 0.099 for the locus Hpms 1-165 to 0.806 for the locus CAMS-679. All of the SSRs examined were informative in characterizing the genotypic variance of the samples while 12 were more informative with higher PIC values (> 0.6). There was a wide range of genetic diversity varied from 0.117 (HpmsE075) to 0.806 (CAMS-647), whereas the highest (1.713) and the lowest (0.205) value of Shannon’s Information Index was registered in the locus CAMS-679 and Hpms 1-165, respectively. There was a higher degree of genetic differentiation (0.927) and a lower amount of gene flow (0.010). Nei’s genetic distance (GD) varied from 0.100 to 0.990. Among 96 cultivars, 55 had distinct status in the dendrogram with higher GD values (> 0.6), while 41 cultivars showed a close relationship and yielded lower GD values.

Author Biographies

  • Md. Rezwan MOLLA, Bangladesh Agricultural Research Institute, Bangladesh
    Plant Genetic Resources Centre and Senior Scientific Officer
  • Iftekhar AHMED, Bangladesh Agricultural Research Institute, Bangladesh
    Plant Genetic Resources Centre and Senior Scientific Officer
  • Md. Motiar ROHMAN, Bangladesh Agricultural Research Institute, Bangladesh
    Plant Breeding Division and Senior Scientific Officer
  • Mohammad Amdadul HAQUE, Bangladesh Agricultural Research Institute, Bangladesh
    Pomology division and Senior Scientific Officer
  • Shah Md. Monir HOSSAIN, Bangladesh Agricultural Research Council, Bangladesh
    Crops Division and Senior Scientific Officer
  • Lutful HASSAN, Bangladesh Agricultural University, Bangladesh
    Department of Genetics and Plant Breeding and Professor


Abouzied, H. M., Eldemery, S. M. M., & Abdellatif, K. F. (2013). SSR-based genetic diversity assessment in tetraploid and hexaploid wheat populations. Biotechnology Journal International, 390–404.

Anumalla, M., Roychowdhury, R., Geda, C. K., Mazid, M., & Rathoure, A. K. (2015). Utilization of plant genetic resources and diversity analysis tools for sustainable crop improvement with special emphasis on rice. International Journal of Advanced Research, 3(3), 1155–1175.

BBS. (2021). Statistical Year Book Bangladesh.

Cao, T., Duprez, E., Borden, K. L. B., Freemont, P. S., & Etkin, L. D. (1998). Ret finger protein is a normal component of PML nuclear bodies and interacts directly with PML. Journal of Cell Science, 111(10), 1319–1329.

Chen, X., Min, D., Yasir, T. A., & Hu, Y. G. (2012). Genetic diversity, population structure and linkage disequilibrium in elite chinese winter wheat investigated with SSR markers. PLoS ONE, 7(9), 1–9.

Dhaliwal, M. S., Yadav, A., & Jindal, S. K. (2014). Molecular characterization and diversity analysis in chilli pepper using simple sequence repeats (SSR) markers. African Journal of Biotechnology, 13(31), 3137–3143.

Di Dato, F., Parisi, M., Cardi, T., & Tripodi, P. (2015). Genetic diversity and assessment of markers linked to resistance and pungency genes in Capsicum germplasm. Euphytica, 204(1), 103–119.

Farhad, M., Hasanuzzaman, M., Biswas, B. K., Arifuzzaman, M., & Islam, M. M. (2010). Genetic divergence in chilli (Capsicum annuum L.). Bangladesh Research Publication Journal, 3(3), 1045–1058.

Hernández-Pérez, T., Gómez-García, M. del R., Valverde, M. E., & Paredes-López, O. (2020). Capsicum annuum (hot pepper): An ancient Latin-American crop with outstanding bioactive compounds and nutraceutical potential. A review. Comprehensive Reviews in Food Science and Food Safety, 19(6), 2972–2993.

Hossain, S. M., Habiba, U., Bhuyan, S. I., Haque, M. S., Begum, S. N., & Hossain, D. M. (2014). DNA fingerprinting and genetic diversity analysis of chilli germplasm using microsatellite markers. Biotechnology, 13(4), 174–180.

Islam, M. N., Molla, M. R., Rohman, M. M., Hasanuzzaman, M., Islam, S. M. N., & Rahman, L. (2012). DNA fingerprinting and genotyping of cotton varieties using SSR markers. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 40(2), 261–265.

Islam, M. Z., Khalequzzaman, M., Bashar, M. K., Ivy, N. A., Mian, M. A. K., Pittendrigh, B. R., Haque, M. M., & Ali, M. P. (2018). Variability assessment of aromatic rice germplasm by pheno-genomic traits and population structure analysis. Scientific Reports, 8(1), 1–14.

Jain, S., Kumar, A., Mamidi, S., & McPhee, K. (2014). Genetic diversity and population structure among pea (Pisum sativum L.) cultivars as revealed by simple sequence repeat and novel genic markers. Molecular Biotechnology, 56(10), 925–938.

Lee, C. J., Yoo, E. Y., Shin, J., Lee, J., Hwang, H. S., & Kim, B. D. (2005). Erratum: Non-pungent Capsicum contains a deletion in the capsaicinoid synthetase gene, which allows early detection of pungency with SCAR markers (Molecules and Cells 19, 2 (262-267)). Molecules and Cells, 20(2), 303.

Mimura, Y., Inoue, T., Minamiyama, Y., & Kubo, N. (2012). An SSR-based genetic map of pepper (Capsicum annuum L.) serves as an anchor for the alignment of major pepper maps. Breeding Science, 62(1), 93–98.

Minamiyama, Y., Tsuro, M., & Hirai, M. (2006). An SSR-based linkage map of Capsicum annuum. Molecular Breeding, 18(2), 157–169.

Molla, K. A., Bhusan, A. B., Ganie, S. A., & Mondal, T. K. (2015). Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.). BMC Plant Biology, 15(1), 1–11.

Molla, M. R., Ahmed, I., Rahman, S., Hossain, M. A., Salam, M. A., Chowdhury, M. A. Z., & Rohman, M. M. (2017). Genetic diversity among muskmelon (Cucumis melo L.) germplasm in Bangladesh as revealed by microsatellite markers. African Journal of Agricultural Research, 12(44), 3203–3213.

Molla, M. R., Ahmed, I., Rohman, M. M., Hossain, M. A., & Chowdhury, M. A. Z. (2016). Genetic diversity analysis and DNA fingerprinting of Mungbean (Vigna radiata L.) genotypes using SSR markers. Plant Science, 6(4), 153–164.

Molla, Md Rezwan, Rohman, M. M., Monsur, M. B., Hasanuzzaman, M., & Hassan, L. (2021). Screening and assessment of selected chilli (Capsicum annuum L.) genotypes for drought tolerance at seedling stage. Phyton, 90(5), 1425.

Nei, M. (1972). Genetic distance between populations. The American Naturalist, 106(949), 283–292.

Pickersgill, B. (1991). Cytogenetics and evolution of Capsicum L. In: Tsuchiya T, Gupta PK (Editors), Chromosome Engineering in Plants: Genetics, Breeding, Evolution Part B. Elsevier, Amsterdam. pp. 139-160.

Rahman, M., Sohag, M., & Rahman, L. (2010). Microsatellite based DNA fingerprinting of 28 local rice (Oryza sativa L.) varieties of Bangladesh. Journal of the Bangladesh Agricultural University, 8(1), 7–17.

Roychowdhury, R., Taoutaou, A., Hakeem, K. R., Ragab, M., Gawwad, A., & Tah, J. (2014). Molecular Marker-Assisted Technologies for Crop Improvement. In Crop improvement in the era of climate change (Vol. 2, Issue April 2016, pp. 241–258).

Saghai-Maroof, M. A., Soliman, K. M., Jorgensen, R. A., & Allard, R. W. (1984). Ribosomal DNA spacer-length polymorphisms in barley : Mendelian inheritance , chromosomal location , and population dynamics. Proceedings of National Academy Science, 81(December), 8014–8018.

Sharmin, A., Hoque, M. E., Haque, M. M., & Khatun, F. (2018). Molecular diversity analysis of some chilli (Capsicum spp.) genotypes using SSR markers. American Journal of Plant Sciences, 09(03), 368–379.

Sundaram, R. M., Naveenkumar, B., Biradar, S. K., Balachandran, S. M., Mishra, B., Ilyasahmed, M., Viraktamath, B. C., Ramesha, M. S., & Sarma, N. P. (2008). Identification of informative SSR markers capable of distinguishing hybrid rice parental lines and their utilization in seed purity assessment. Euphytica, 163(2), 215–224.

van Zonneveld, M., Scheldeman, X., Escribano, P., Viruel, M. A., van Damme, P., Garcia, W., Tapia, C., Romero, J., Sigueñas, M., & Hormaza, J. I. (2012). Mapping genetic diversity of cherimoya (Annona cherimola Mill.): Application of spatial analysis for conservation and use of plant genetic resources. PLoS ONE, 7(1).

Yi, G., Lee, J. M., Lee, S., Choi, D., & Kim, B. D. (2006). Exploitation of pepper EST-SSRs and an SSR-based linkage map. Theoretical and Applied Genetics, 114(1), 113–130.



30. 12. 2022



Original Scientific Article

How to Cite

MOLLA, M. R., AHMED, I., ROHMAN, M. M., HAQUE, M. A., HOSSAIN, S. M. M., & HASSAN, L. (2022). Genetic diversity in - chilli (Capsicum annuum L.) based on microsatellite markers: An evaluation of Bangladeshi germplasm. Acta Agriculturae Slovenica, 118(4), 1–20.

Similar Articles

1-10 of 539

You may also start an advanced similarity search for this article.

Most read articles by the same author(s)